Thank you for you reply.
There are many causes of painful intercourse that range anywhere from psychological to physical.
Given the fact that most pain is throughout intercourse (and not during penetration) it can rule out several causes right away.
Other causes which are more common could be contractions of the uterus during intercourse which will cause pain, overgrowth of tissue in the vagina causing what is known as hyperplasia, and even though you said she seems to be well lubricated, inadequate lubrication is a very common problem (especially if she is approaching menopause). Water based lubricants are recommended (do not use Vaseline as it can actually cause irritation to vaginal tissue).
I am also going to suggest a possibility of a psychological factor even though this is not very common. I dont know your relationship and how you feel towards each other so I am unable to make a stronger point on this issue.
I understand that this is a delicate question, however, without your wife's willingness to discuss this issue with her gynecologist, a cause may not be found. Most of the time there is a physical cause for painful intercourse and that is why it is important to discuss and address with her doctor. She might want to consider seeing Urogynecologist which is a subspecialty of gynecology and might be more beneficial but if not available any gynecologist should be able to assist.
Inadequate and incomplete sexual relationship definitely puts a strain on a relationship and if your wife is interested in preserving a long-lasting and happy marriage, unfortunately she will need to turn to her physician for help. I am pretty certain that this is not anything you are doing wrong.
I hope this information is helpful to you and turns you towards the right direction. Please feel free to let me know if you might have any other questions I might be able to assist you with.
inadequate lubrication (water-based lubricant, not Vaseline which can be harmful to vaginal tissue)
overgrowth of vaginal tissue